We estimated the proportion of diarrhea attributable to cholera and other pathogens during the rainy and dry seasons in patients seen in two urban health settings: a cholera treatment center (CTC) and oral rehydration points (ORPs). During April 1, 2011-November 30, 2012, stool samples were collected from 1,206 of 10,845 patients who came to the GHESKIO CTC or to the community ORPs with acute diarrhea, cultured for Vibrio cholerae, and tested by multiplex polymerase reaction. Vibrio cholerae was isolated from 409 (41.8%, 95% confidence interval [CI] = 38.7-44.9%) of the 979 specimens from the CTC and in 45 (19.8%, 95% CI = 14.8-25.6%) of the 227 specimens from the ORPs. Frequencies varied from 21.4% (95% CI = 16.6-26.7%) during the dry season to 46.8% (95% CI = 42.9-50.7%) in the rainy season. Shigella, enterotoxigenic Escherichia coli, rotavirus, and Cryptosporidium were frequent causes of diarrhea in children less than five years of age.